genomeIntervals (version 1.28.0)

interval_overlap: Assess overlap from one set of genomic intervals to another

Description

Given two objects, a 'from' and a 'to', assess which intervals in 'to' overlap which of 'from'.

Usage

"interval_overlap"( from, to, check_valid = TRUE )
"interval_overlap"( from, to, check_valid = TRUE )

Arguments

from

A Genome_intervals or Genome_intervals_stranded object.

to

A Genome_intervals or Genome_intervals_stranded object.

check\_valid

Should validObject be called before passing to compiled code?

Value

A list, with one element for each row of from. The elements are vectors of indices, indicating which to rows overlap each from. A list element of length 0 indicates a from with no overlapping to intervals.

Details

A wrapper calling intervals:interval_overlap by seq_name and by strand (if both to and from are "Genome_intervals_stranded" objects).

Examples

data(gen_ints)	 
# i as entered
i

# i in close_intervals notation
close_intervals(i)
 
# j in close_intervals notation
close_intervals(j)
 
# list of intervals of j overlapping intervals of i
interval_overlap(i,j)